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- PDB-5an1: Crystallographic structure of the Glutathione S-Transferase from ... -

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Basic information

Entry
Database: PDB / ID: 5an1
TitleCrystallographic structure of the Glutathione S-Transferase from Litopenaeus vannamei complexed with Glutathione
ComponentsGLUTATHIONE S-TRANSFERASE
KeywordsTRANSFERASE / GLUTATHIONE / XENOBIOTIC / DISULPHIDE BOND GST / MU- CLASS
Function / homology
Function and homology information


glutathione transferase / glutathione transferase activity
Similarity search - Function
Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, Mu class / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / glutathione transferase
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJuarez-Martinez, A.B. / Sotelo-Mundo, R. / Rudino-Pinera, E.
CitationJournal: J. Biochem. Mol. Toxicol. / Year: 2017
Title: Crystal structure of a class-mu glutathione S-transferase from whiteleg shrimp Litopenaeus vannamei: structural changes in the xenobiotic binding H-site may alter the spectra of molecules bound.
Authors: Juarez-Martinez, A.B. / Sotelo-Mundo, R.R. / Rudino-Pinera, E.
History
DepositionSep 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTATHIONE S-TRANSFERASE
B: GLUTATHIONE S-TRANSFERASE
C: GLUTATHIONE S-TRANSFERASE
D: GLUTATHIONE S-TRANSFERASE
E: GLUTATHIONE S-TRANSFERASE
F: GLUTATHIONE S-TRANSFERASE
G: GLUTATHIONE S-TRANSFERASE
H: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,87816
Polymers204,4208
Non-polymers2,4598
Water36,6792036
1
D: GLUTATHIONE S-TRANSFERASE
E: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7204
Polymers51,1052
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-21.5 kcal/mol
Surface area19470 Å2
MethodPISA
2
B: GLUTATHIONE S-TRANSFERASE
G: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7204
Polymers51,1052
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-20.3 kcal/mol
Surface area19080 Å2
MethodPISA
3
C: GLUTATHIONE S-TRANSFERASE
hetero molecules

F: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7204
Polymers51,1052
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3590 Å2
ΔGint-19.7 kcal/mol
Surface area19030 Å2
MethodPISA
4
F: GLUTATHIONE S-TRANSFERASE
hetero molecules

C: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7204
Polymers51,1052
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3590 Å2
ΔGint-19.7 kcal/mol
Surface area19030 Å2
MethodPISA
5
A: GLUTATHIONE S-TRANSFERASE
H: GLUTATHIONE S-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7204
Polymers51,1052
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-21.9 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.025, 101.943, 166.595
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GLUTATHIONE S-TRANSFERASE /


Mass: 25552.455 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 1-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q49SB0, glutathione transferase
#2: Chemical
ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2036 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 % / Description: NONE
Crystal growpH: 8 / Details: 0.2M SODIUM FORMATE,20% PEG3350, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 135630 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 19.93 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.14
Reflection shellResolution: 2→2.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.09 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6GSW

6gsw


Resolution: 2→38.356 Å / SU ML: 0.27 / σ(F): 1.36 / Phase error: 30.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 2064 1.5 %
Rwork0.2138 --
obs0.2146 135411 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.61 Å2
Refinement stepCycle: LAST / Resolution: 2→38.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14376 0 160 2036 16572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914987
X-RAY DIFFRACTIONf_angle_d1.24620240
X-RAY DIFFRACTIONf_dihedral_angle_d14.6985578
X-RAY DIFFRACTIONf_chiral_restr0.0532117
X-RAY DIFFRACTIONf_plane_restr0.0072580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04650.30371000.23498834X-RAY DIFFRACTION97
2.0465-2.09770.32431590.24278815X-RAY DIFFRACTION97
2.0977-2.15440.3181370.25148887X-RAY DIFFRACTION97
2.1544-2.21780.27641320.25348955X-RAY DIFFRACTION97
2.2178-2.28940.38711180.34477484X-RAY DIFFRACTION82
2.2894-2.37120.31331270.23168937X-RAY DIFFRACTION98
2.3712-2.46610.24841490.22128939X-RAY DIFFRACTION98
2.4661-2.57830.28621350.2119005X-RAY DIFFRACTION98
2.5783-2.71420.27781500.22288957X-RAY DIFFRACTION98
2.7142-2.88420.27071500.2198998X-RAY DIFFRACTION98
2.8842-3.10680.25171250.22229095X-RAY DIFFRACTION98
3.1068-3.41930.24121580.21179061X-RAY DIFFRACTION99
3.4193-3.91370.23331420.19459000X-RAY DIFFRACTION98
3.9137-4.92920.24711390.1729121X-RAY DIFFRACTION99
4.9292-38.36350.21361430.18279259X-RAY DIFFRACTION99

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